|
| Status |
Public on Jul 12, 2023 |
| Title |
RNAseq_BMP2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreatic islets
strain: C57BL/6NRj
Sex: male
age: 12 weeks
treatment: BMP2 10 d
|
| Treatment protocol |
Islets were cultured in the absence or presence of 50ng/ml BMP2
|
| Growth protocol |
Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and BMP2 were changed every 5th day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvest using Rneasy Micro Kit (Qiagen) according to the manufacturer instructions.
RNA libraries were constructed from 35ng of isolated RNA using TruSeq Stranded mRNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Single-end 50bp RNA-seq reads were mapped to the UCSC mouse genome (mm9) by STAR v. 2.4.0 (--outSAMstrandField intronMotif--outFilterMultimapNmax 1 --rethread 5), allowing for up to 10 mismatches (default by STAR)
Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Expression levels of all genes were estimated by Cufflinks v2.2.1 (-p 6 -G $gtf_file --max-bundle-frags 1000000000) using only the reads with exact matches. Differential gene expression was performed using Cuffdiff (Cufflinks v2.2.1), with FDR < 0.05 considered significant.
In homer, function "makeUCSCfile" was used to generate bigWig files
Assembly: mm9
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Jul 12, 2023 |
| Contact name |
Matthew Wortham |
| E-mail(s) |
mwortham@ucsd.edu
|
| Phone |
8582460588
|
| Organization name |
University of California, San Diego
|
| Lab |
Maike Sander
|
| Street address |
2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE216231 |
Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding {RNA-seq] |
| GSE216233 |
Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding |
|
| Relations |
| BioSample |
SAMN31391441 |
| SRA |
SRX17970143 |
